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Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated , the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear . To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe , ...	It has recently become apparent that most introns are removed from pre-mRNA while the transcript is still engaged with RNA polymerase II ( RNAPII ) . To gain insight into possible roles for chromatin in co-transcriptional splicing , we generated a genome-wide genetic interaction map in fission yeast and uncovered numer...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast
Genomic loci with regulatory potential can be annotated with various properties . For example , genomic sites bound by a given transcription factor ( TF ) can be divided according to whether they are proximal or distal to known promoters . Sites can be further labeled according to the cell types and conditions in which...	Transcription factor proteins control gene expression by recognizing and interacting with short DNA sequence patterns in regulatory regions on the genome . Current genomics experiments allow us to find regulatory regions associated with a particular biochemical activity over the entire genome; for example , all regions...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "binding", "cell", "physiology", "chemical", "characterization", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "genome", "analysis", "transcription", "factors", "genome", "annotation", "sequence", "motif", "analysis", "epigenetics", "c...	2017	Deconvolving sequence features that discriminate between overlapping regulatory annotations
Characterizing the force of infection ( FOI ) is an essential part of planning cost effective control strategies for zoonotic diseases . Echinococcus multilocularis is the causative agent of alveolar echinococcosis in humans , a serious disease with a high fatality rate and an increasing global spread . Red foxes are h...	Human alveolar echinococcosis ( AE ) is caused by the fox tapeworm E . multilocularis and has a high fatality rate if untreated . The frequency of the tapeworm in foxes can be reduced through the regular distribution of anthelmintic baits and thus decrease the risk of zoonotic transmission . Here , we estimate the forc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "echinococcosis", "infectious", "diseases", "veterinary", "epidemiology", "mathematics", "environmental", "epidemiology", "epidemiology", "statistics", "spatial", "epidemiology", "biostatistics", "epidemiological", "methods", "parasitic", "diseases", "veterinary", "...	2014	Dynamics of the Force of Infection: Insights from Echinococcus multilocularis Infection in Foxes
The gene encoding the forkhead box transcription factor , FOXP2 , is essential for developing the full articulatory power of human language . Mutations of FOXP2 cause developmental verbal dyspraxia ( DVD ) , a speech and language disorder that compromises the fluent production of words and the correct use and comprehen...	Do special “human” genes provide the biological substrate for uniquely human traits , such as language ? Genetic aberrations of the human FoxP2 gene impair speech production and comprehension , yet the relative contributions of FoxP2 to brain development and function are unknown . Songbirds are a useful model to addres...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "neuroscience", "genetics", "and", "genomics" ]	2007	Incomplete and Inaccurate Vocal Imitation after Knockdown of FoxP2 in Songbird Basal Ganglia Nucleus Area X
During the development of neural circuitry , neurons of different kinds establish specific synaptic connections by selecting appropriate targets from large numbers of alternatives . The range of alternative targets is reduced by well organised patterns of growth , termination , and branching that deliver the terminals ...	Axons and dendrites of synaptic partners must be targeted to a common region of the developing neural network so that appropriate connections can be formed . The mechanisms underlying this targeting are incompletely understood . We showed previously that a positional cue ( Slit ) acting in the medio-lateral axis of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/pattern", "formation", "neuroscience/neurodevelopment", "developmental", "biology", "neuroscience/sensory", "systems" ]	2009	Positional Cues in the Drosophila Nerve Cord: Semaphorins Pattern the Dorso-Ventral Axis
Botrytis cinerea is the causal agent of gray mold diseases in a range of dicotyledonous plant species . The fungus can reproduce asexually by forming macroconidia for dispersal and sclerotia for survival; the latter also participate in sexual reproduction by bearing the apothecia after fertilization by microconidia . L...	Both fungal pathogens and their host plants respond to light , which represents an important environmental cue . Unlike plants using light for energy generation , filamentous fungi use light , or its absence , as a general signal for orientation ( night/day , underground/on the surface ) . Therefore , dependent on the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "regulation", "host-pathogen", "interaction", "microbiology", "fungal", "physiology", "gene", "function", "fungal", "evolution", "molecular", "genetics", "fungal", "reproduction", "mycology", "signaling", "in", "cellular", "processes", "transcriptional", "signaling"...	2014	The Transcription Factor BcLTF1 Regulates Virulence and Light Responses in the Necrotrophic Plant Pathogen Botrytis cinerea
While many models of biological object recognition share a common set of “broad-stroke” properties , the performance of any one model depends strongly on the choice of parameters in a particular instantiation of that model—e . g . , the number of units per layer , the size of pooling kernels , exponents in normalizatio...	One of the primary obstacles to understanding the computational underpinnings of biological vision is its sheer scale—the visual system is a massively parallel computer , comprised of billions of elements . While this scale has historically been beyond the reach of even the fastest super-computing systems , recent adva...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "science/natural", "and", "synthetic", "vision", "neuroscience/natural", "and", "synthetic", "vision", "neuroscience/sensory", "systems" ]	2009	A High-Throughput Screening Approach to Discovering Good Forms of Biologically Inspired Visual Representation
Development of prefrontal and other higher-order association cortices is associated with widespread changes in the cortical transcriptome , particularly during the transitions from prenatal to postnatal development , and from early infancy to later stages of childhood and early adulthood . However , the timing and long...	Prolonged maturation of the human cerebral cortex , which extends into the third decade of life , is critical for proper development of executive functions such as higher-order problem-solving and complex cognition . Little is known about changes of post-mitotic neurons during this prolonged maturation period , includi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "genetics", "epigenetics", "biology", "computational", "biology" ]	2013	Coordinated Cell Type–Specific Epigenetic Remodeling in Prefrontal Cortex Begins before Birth and Continues into Early Adulthood
Many bacteria mediate important life-style decisions by varying levels of the second messenger c-di-GMP . Behavioral transitions result from the coordination of complex cellular processes such as motility , surface adherence or the production of virulence factors and toxins . While the regulatory mechanisms responsible...	Bacterial processes like virulence , motility or biofilm formation are governed by the second messenger c-di-GMP . In most bacteria , c-di-GMP is produced and degraded by a complex network comprising dozens of enzymes . This has hindered a comprehensive analysis of the cellular role of c-di-GMP . Here we mutate the ent...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Bi-modal Distribution of the Second Messenger c-di-GMP Controls Cell Fate and Asymmetry during the Caulobacter Cell Cycle
Classical decision theory postulates that choices proceed from subjective values assigned to the probable outcomes of alternative actions . Some authors have argued that opposite causality should also be envisaged , with choices influencing subsequent values expressed in desirability ratings . The idea is that agents m...	The standard way to explain decisions is the so-called valuation/selection model , which includes 1 ) a value function that calculates desirability for every possible outcome of alternative actions and 2 ) a choice function that integrates outcome values and generates selection probability for every action . In this cl...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "decision", "theory", "classical", "mechanics", "decision", "making", "engineering", "and", "technology", "thermometers", "statistics", "applied", "mathematics", "social", "sciences", "mathematical", "models", "neuroscience", "cognitive", "psychology", "mathematics", "cogni...	2019	Sour grapes and sweet victories: How actions shape preferences
Poly-β ( 1 , 6 ) -N-acetyl-D-glucosamine ( PNAG ) is a major biofilm component of many pathogenic bacteria . The production , modification , and export of PNAG in Escherichia coli and Bordetella species require the protein products encoded by the pgaABCD operon . PgaB is a two-domain periplasmic protein that contains a...	From plaque on teeth to infections in the lungs of cystic fibrosis patients , biofilms are a serious health concern and difficult to eradicate . One of the key building blocks involved in biofilm formation are polymeric sugar compounds that are secreted by the bacteria . Our work focuses on the biopolymer poly-β ( 1 , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "biofilms", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "microbiology", "enzymology", "materials", "science", "glycoside", "hydrolases", "sequence", "motif", "analysis", "oligomers", "macro...	2018	PgaB orthologues contain a glycoside hydrolase domain that cleaves deacetylated poly-β(1,6)-N-acetylglucosamine and can disrupt bacterial biofilms
Hypermutation of the immunoglobulin ( Ig ) genes requires Activation Induced cytidine Deaminase ( AID ) and transcription , but it remains unclear why other transcribed genes of B cells do not mutate . We describe a reporter transgene crippled by hypermutation when inserted into or near the Ig light chain ( IgL ) locus...	It remains an open question how AID-mediated gene diversification is targeted to the immunoglobulin loci . Here we define a cis-acting sequence , named DIVAC for diversification activator , which is required for hypermutation of the Ig light chain gene and sufficient to activate hypermutation at various non-Ig loci in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "cell", "biology", "immunology/genetics", "of", "the", "immune", "system", "molecular", "biology" ]	2009	A cis-Acting Diversification Activator Both Necessary and Sufficient for AID-Mediated Hypermutation
In June 2014 , Suriname faced the first Chikungunya outbreak . Since international reports mostly focus on hospitalized patients , the least affected group , a study was conducted to describe clinical characteristics of mainly outpatients including children . In addition , the cumulative incidence of this first epidemi...	Chikungunya virus is transmitted to humans by mosquito bites and causes fever and joint pain . Chikungunya was first detected in Africa , but recently became a worldwide concern with outbreaks in many ( sub ) -tropical countries . We report the characteristics of the first outbreak in Suriname ( 2014–2015 ) . Mainly no...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "dermatology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "alphaviruses", "headaches", "viruses", "chikun...	2016	First Chikungunya Outbreak in Suriname; Clinical and Epidemiological Features
BALB/c mice are highly susceptible while C57BL/6 are relatively resistant to experimental Trypanosoma congolense infection . Although regulatory T cells ( Tregs ) have been shown to regulate the pathogenesis of experimental T . congolense infection , their exact role remains controversial . We wished to determine wheth...	BALB/c mice are highly susceptible while C57BL/6 is relatively resistant to experimental Trypanosoma congolense infection . Acute death observed in infected BALB/c mice is usually associated with the excessive production of pro-inflammatory cytokines . Regulatory T cells ( Tregs ) have been shown to play a significant ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2012	Regulatory T Cells Enhance Susceptibility to Experimental Trypanosoma Congolense Infection Independent of Mouse Genetic Background
A genome-wide screen for large structural variants showed that a copy number variant ( CNV ) in the region encoding killer cell immunoglobulin-like receptors ( KIR ) associates with HIV-1 control as measured by plasma viral load at set point in individuals of European ancestry . This CNV encompasses the KIR3DL1-KIR3DS1...	There is marked intrinsic variation in the extent to which individuals are able to control HIV-1 . We have identified a genetic copy number variable region ( CNV ) in humans that plays a significant role in the control of HIV-1 . This CNV is located in the genomic region that encodes the killer cell immunoglobulin-like...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genetics", "of", "the", "immune", "system", "genetics", "molecular", "genetics", "biology", "human", "genetics", "gene", "duplication", "immunology", "genetics", "and", "genomics" ]	2011	Copy Number Variation of KIR Genes Influences HIV-1 Control
The transition from vegetative growth to multicellular development represents an evolutionary hallmark linked to an oxidative stress signal and controlled protein degradation . We identified the Sem1 proteasome subunit , which connects stress response and cellular differentiation . The sem1 gene encodes the fungal coun...	The cellular ubiquitin-proteasome pathway is essential to control cell cycle , gene expression or the response to oxidative stress . Sem1 is conserved in eukaryotes from single cell yeasts to humans as intrinsically disordered and multifunctional protein . Sem1 supports the assembly of several multiprotein complexes bu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cellular", "stress", "responses", "aspergillus", "oxidative", "stress", "fungal", "genetics", "cell", "processes", "dna", "transcription", "aspergillus", "nidulans", "mutation", "fungi", "experimental", "organism", "systems", "mitochondria", "bioenergetics", "cellular", ...	2018	Sem1 links proteasome stability and specificity to multicellular development
Many cancers are understood to be the product of multiple somatic mutations or other rate-limiting events . Multistage clonal expansion ( MSCE ) models are a class of continuous-time Markov chain models that capture the multi-hit initiation–promotion–malignant-conversion hypothesis of carcinogenesis . These models have...	Parameter estimation from data is an important part of mathematical modeling , and structural identifiability is the study of what parametric information exists , for a given model , in ideal data . Unfortunately , for a variety of reasons , there is often less information available in our real data sets . The study of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "markov", "models", "cell", "processes", "cancers", "and", "neoplasms", "gastrointestinal", "tumors", "oncology", "systems", "science", "mathematics", "statistics", "(mathematics)", "epigenetics", "cancer", "epid...	2017	Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis
The protozoan parasite Leishmania possesses a single flagellum , which is remodelled during the parasite’s life cycle from a long motile flagellum in promastigote forms in the sand fly to a short immotile flagellum in amastigotes residing in mammalian phagocytes . This study examined the protein composition and in vivo...	Leishmania are protozoan parasites , transmitted between mammals by the bite of phlebotomine sand flies . Promastigote forms in the sand fly have a long flagellum , which is motile and used for anchoring the parasites to prevent clearance with the digested blood meal remnants . To dissect flagellar functions and their ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "motility", "medicine", "and", "health", "sciences", "swimming", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "sand", "flies", "flagellar", "motility", "parasitic", "diseases", "protozoan", "life", "cycles", "parasitic", "protozoans...	2019	Genetic dissection of a Leishmania flagellar proteome demonstrates requirement for directional motility in sand fly infections
Caloric restriction extends lifespan , an effect once thought to involve attenuation of reactive oxygen species ( ROS ) generated by aerobic metabolism . However , recent evidence suggests that caloric restriction may in fact raise ROS levels , which in turn provides protection from acute doses of oxidant through a pro...	Reactive oxygen species ( ROS ) damage a variety of structures within the cell , resulting in disease and aging . In a seemingly paradoxical effect termed adaptation , it is possible to prevent damage caused by ROS by pre-treating the cell with a small amount of oxidant . We studied this process in order to identify th...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/systems", "biology", "computational", "biology/transcriptional", "regulation", "cell", "biology/cellular", "death", "and", "stress", "responses", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "expression", ...	2009	Genome-Wide Fitness and Expression Profiling Implicate Mga2 in Adaptation to Hydrogen Peroxide
Sole reliance on one drug , Praziquantel , for treatment and control of schistosomiasis raises concerns about development of widespread resistance , prompting renewed interest in the discovery of new anthelmintics . To discover new leads we designed an automated label-free , high content-based , high throughput screen ...	Schistosomiasis is a severe helminth infection affecting an estimated 600 million people . The one drug widely available , praziquantel ( PZQ ) , is not ideal . PZQ kills the adult worms but not the developing juveniles so the treated patient may not be cured long-term . In addition , use of repeated mass treatment cam...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "drug", "research", "and", "development", "science", "policy", "technology", "development", "drugs", "and", "devices", "pharmacology", "biology", "zoology", "drug", "discovery", "helminthology" ]	2012	Whole Organism High-Content Screening by Label-Free, Image-Based Bayesian Classification for Parasitic Diseases
Menopause , the permanent cessation of ovulation , occurs in humans well before the end of the expected lifespan , leading to an extensive post-reproductive period which remains a puzzle for evolutionary biologists . All human populations display this particularity; thus , it is difficult to empirically evaluate the co...	In all human populations , regardless of environmental and socioeconomic conditions , menopause occurs in women well before the end of their expected lifespan . Conversely , extensive post-reproductive life-span is rare in other species; except in some cetaceans . Evolutionary theory predicts that menopause and extensi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "children", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "ecological", "niches", "maternal", "health", "obstetrics", "and", "gynecology", "neuroscience", "endocrine", "physiology", "age", "groups", "women's", "health", "theoret...	2017	Grandmothering and cognitive resources are required for the emergence of menopause and extensive post-reproductive lifespan
Retroviral capsid recognition by Trim5 blocks productive infection . Rhesus macaques harbor three functionally distinct Trim5 alleles: Trim5αQ , Trim5αTFP and Trim5CypA . Despite the high degree of amino acid identity between Trim5αQ and Trim5αTFP alleles , the Q/TFP polymorphism results in the differential restriction...	TRIM5α is an intrinsic immunity protein that blocks retrovirus infection through a specific interaction with the viral capsid . Uniquely among primates , rhesus macaques harbor three functionally distinct kinds of Trim5 alleles: rhTrim5αTFP , rhTrim5αQ and rhTrim5CypA . SIVmac239 , a simian immunodeficiency virus that ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "models", "of", "infection", "immunodeficiency", "viruses", "mechanisms", "of", "resistance", "and", "susceptibility", "model", "organisms", "viral", "immune", "evasion", "virology", "genetics", "viral", "structure", "biology", "microbiology", "evolutionary", ...	2013	Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5α Specificity
An animal’s ability to survive depends on its sensory systems being able to adapt to a wide range of environmental conditions , by maximizing the information extracted and reducing the noise transmitted . The visual system does this by adapting to luminance and contrast . While luminance adaptation can begin at the ret...	An animal’s ability to survive depends on its ability to adapt to a wide range of light conditions , by maximizing the information flow through the retina . Here , we show a new form of adaptation in cone photoreceptors that helps them optimize the information they transmit by adjusting their response kinetics to bette...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fourier", "analysis", "medicine", "and", "health", "sciences", "membrane", "potential", "social", "sciences", "light", "electrophysiology", "neuroscience", "electromagnetic", "radiation", "systems", "science", "mathematics", "luminance", "visible", "light", "vision", "re...	2017	A novel mechanism of cone photoreceptor adaptation
A recent paper ( Nehrt et al . , PLoS Comput . Biol . 7:e1002073 , 2011 ) has proposed a metric for the “functional similarity” between two genes that uses only the Gene Ontology ( GO ) annotations directly derived from published experimental results . Applying this metric , the authors concluded that paralogous genes ...	Understanding gene function—how individual genes contribute to the biology of an organism at the molecular , cellular and organism levels—is one of the primary aims of biomedical research . It has been a longstanding tenet of model organism research that experimental knowledge obtained in one organism is often applicab...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genomics", "model", "organisms", "biology", "computational", "biology" ]	2012	On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report
During oogenesis in metazoans , the meiotic divisions must be coordinated with development of the oocyte to ensure successful fertilization and subsequent embryogenesis . The ways in which the mitotic machinery is specialized for meiosis are not fully understood . cortex , which encodes a putative female meiosis-specif...	Meiosis is a modified cell cycle that generates four gametes , each containing half the genetic content of the parent cell , through a reductional division followed by an equational division without an intervening DNA synthesis phase . During oogenesis of multicellular organisms , proper coordination of the meiotic div...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "drosophila", "cell", "biology", "developmental", "biology", "molecular", "biology" ]	2007	Developmental Role and Regulation of cortex, a Meiosis-Specific Anaphase-Promoting Complex/Cyclosome Activator
The RRM-type RNA-binding protein Mei2 is a master regulator of meiosis in fission yeast , in which it stabilizes meiosis-specific mRNAs by blocking their destruction . Artificial activation of Mei2 can provoke the entire meiotic process , and it is suspected that Mei2 may do more than the stabilization of meiosis-speci...	Hundreds of genes are newly expressed during meiosis , a process to form gametes , and the control of meiosis-specific gene expression is not simple . The master regulator of meiosis in fission yeast , Mei2 , blocks an RNA destruction system that selectively degrades meiosis-specific mRNAs , highlighting the importance...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "cellular", "stress", "responses", "cell", "division", "cell", "biology", "gene", "expression", "biology", "molecular", "cell", "biology", "molecular", "biology" ]	2011	The Fission Yeast Stress-Responsive MAPK Pathway Promotes Meiosis via the Phosphorylation of Pol II CTD in Response to Environmental and Feedback Cues
The interactions that occur during HIV Pr55Gag oligomerization and genomic RNA packaging are essential elements that facilitate HIV assembly . However , mechanistic details of these interactions are not clearly defined . Here , we overcome previous limitations in producing large quantities of full-length recombinant Pr...	Formation of any virus particle will require energy , yet the precise biophysical properties that drive the formation of HIV particles remain undefined . Isothermal titration calorimetry ( ITC ) is a biophysical technique that is the gold standard to reveal parameters governing biochemical and biophysical reaction . Ho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rna-binding", "proteins", "medicine", "and", "health", "sciences", "rna", "sequences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "enthalpy", "rna", "viruses", "sequence", "motif", ...	2017	The thermodynamics of Pr55Gag-RNA interaction regulate the assembly of HIV
In eukaryotic organisms , histones are dynamically exchanged independently of DNA replication . Recent reports show that different coding regions differ in their amount of replication-independent histone H3 exchange . The current paradigm is that this histone exchange variability among coding regions is a consequence o...	During nucleosome disassembly and reassembly , evicted histones are exchanged with newly synthesized histones . Histone exchange occurs in several DNA metabolism processes , including replication , transcription , and repair . Recent reports from several labs show that replication-independent histone H3 exchange in yea...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "biology/histone", "modification", "cell", "biology/gene", "expression", "computational", "biology/transcriptional", "regulation", "molecular", "biology/transcription", "elongation", "genetics", "and", "genomics/epigenetics", "molecular", "biology/chromatin", "structur...	2009	Evidence for Gene-Specific Rather Than Transcription Rate–Dependent Histone H3 Exchange in Yeast Coding Regions
Epidemiological studies have reported a higher incidence of rare disorders involving imprinted genes among children conceived using assisted reproductive technology ( ART ) , suggesting that ART procedures may be disruptive to imprinted gene methylation patterns . We examined intra- and inter-individual variation in DN...	We have screened a population of children conceived in vitro for epigenetic alterations at two loci that carry parent-of-origin specific methylation marks . We made the observation that epigenetic variability was greater in extraembryonic tissues than embryonic tissues in both groups , as has also been demonstrated in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "developmental", "biology/developmental", "molecular", "mechanisms", "molecular", "biology/dna", "methylation", "genetics", "and", "genomics/gene", "expression" ]	2010	Inter- and Intra-Individual Variation in Allele-Specific DNA Methylation and Gene Expression in Children Conceived using Assisted Reproductive Technology
It is well established that persistent viral infection may impair cellular function of specialized cells without overt damage . This concept , when applied to neurotropic viruses , may help to understand certain neurologic and neuropsychiatric diseases . Borna disease virus ( BDV ) is an excellent example of a persiste...	When a virus enters the brain , it most often induces inflammation , fever , and brain injury , all signs that are indicative of acute encephalitis . Under certain conditions , however , some neurotropic viruses may cause disease in a subtler manner . The Borna disease virus ( BDV ) is an excellent example of this seco...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Borna Disease Virus Phosphoprotein Impairs the Developmental Program Controlling Neurogenesis and Reduces Human GABAergic Neurogenesis
Understanding the mechanisms of protein–protein interaction is a fundamental problem with many practical applications . The fact that different proteins can bind similar partners suggests that convergently evolved binding interfaces are reused in different complexes . A set of protein complexes composed of non-homologo...	Interaction between proteins is a fundamental process , generic to most biological pathways . The increasing number of protein–protein complexes with atomic data should help us to understand the major factors that guide protein interactions . In particular , a number of examples are available of similar proteins that i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis" ]	2010	Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way
Object conceptual processing has been localized to distributed cortical regions that represent specific attributes . A challenging question is how object semantic space is formed . We tested a novel framework of representing semantic space in the pattern of white matter ( WM ) connections by extending the representatio...	One of the most challenging questions in cognitive neuroscience is how semantic knowledge , for example , that “scissors” and “knives” are related in meaning , can emerge from primary sensory dimensions such as visual forms . It is often assumed that in the human brain , semantics are stored in regions of the brain cor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "linguistics", "diagnostic", "radiology", "pathology", "and", "laboratory", "medicine", "nervous", "system", "brain", "social", "sciences", "neuroscience", "magnetic", "resonance", "imaging", "brain", "morphometry", "signs", "and...	2018	Semantic representation in the white matter pathway
Dendritic cells ( DCs ) are essential antigen-presenting cells for the induction of immunity against pathogens . However , HIV-1 spread is strongly enhanced in clusters of DCs and CD4+ T cells . Uninfected DCs capture HIV-1 and mediate viral transfer to bystander CD4+ T cells through a process termed trans-infection . ...	Mature dendritic cells ( mDCs ) capture and store infectious HIV-1 and subsequently infect neighboring CD4+ T cells in lymphoid organs . This process , known as trans-infection , is a key contributor to HIV pathogenesis , but the precise mechanism and the identity of the receptor on the mDC surface that recognizes vira...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "glycolipids", "immune", "cells", "viral", "transmission", "and", "infection", "sphingolipids", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "viral", "structure", "viral", "attachment", "virusli...	2012	Siglec-1 Is a Novel Dendritic Cell Receptor That Mediates HIV-1 Trans-Infection Through Recognition of Viral Membrane Gangliosides
The recruitment of RNA-Pol-II to the transcription start site ( TSS ) is an important step in gene regulation in all organisms . Core promoter elements ( CPE ) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors ( TFs ) . However , only a minority of animal prom...	Gene transcription is a complex process that starts with the recruitment and positioning of Pol-II enzyme at the transcription start site ( TSS ) . Specific promoter sequences , known as core promoter elements ( CPEs ) facilitate this process . Surprisingly , only a fraction of promoters contain them . It is still unkn...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "invertebrates", "caenorhabditis", "invertebrate", "genomics", "animals", "animal", "models", "nucleosome", "mapping", "caenorhabditis", "elegans", "drosophila", "melanogaster", "model", "organisms", "sequence", "motif", "analysis", "epigenetics", ...	2016	Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters
Nearly all mechanochemical models of the cross-bridge treat myosin as a simple linear spring arranged parallel to the contractile filaments . These single-spring models cannot account for the radial force that muscle generates ( orthogonal to the long axis of the myofilaments ) or the effects of changes in filament lat...	The molecular motor myosin drives the contraction of muscle , but doesn't just produce force in the axis of shortening . Models of muscle contraction have primarily treated myosin as a simple spring oriented parallel to its direction of movement . This assumption does not allow prediction of the relationship between th...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "biophysics/theory", "and", "simulation", "computational", "biology" ]	2010	Axial and Radial Forces of Cross-Bridges Depend on Lattice Spacing
Although leptospirosis is traditionally considered a disease of rural , agricultural and flooded environments , Leptospira spp . are found in a range of habitats and infect numerous host species , with rodents among the most significant reservoirs and vectors . To explore the local ecology of Leptospira spp . in a city...	Leptospirosis is a significant zoonotic disease that is found in a range of environments worldwide , most notably tropical regions prone to flooding . The bacterial agents of this disease , Leptospira spp . , are most often associated with rodents , including species frequently found in urban areas . In cities , rodent...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "vertebrates", "animals", "mammals", "bacterial", "diseases", "urban", ...	2019	Association of rodent-borne Leptospira spp. with urban environments in Malaysian Borneo
Cells infected with dengue virus release a high proportion of immature prM-containing virions . In accordance , substantial levels of prM antibodies are found in sera of infected humans . Furthermore , it has been recently described that the rates of prM antibody responses are significantly higher in patients with seco...	Dengue virus represents a major emerging arboviral pathogen circulating in the ( sub ) tropical regions of the world , putting 2 . 5 billion people at risk of infection . Each of the four circulating serotypes can cause disease ranging from febrile illness to devastating manifestations including dengue hemorrhagic feve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "virology/virulence", "factors", "and", "mechanisms", "virology/host", "invasion", "and", "cell", "entry" ]	2010	Immature Dengue Virus: A Veiled Pathogen?
It has unambiguously been shown that genetic , environmental , demographic , and technical factors may have substantial effects on gene expression levels . In addition to the measured variable ( s ) of interest , there will tend to be sources of signal due to factors that are unknown , unmeasured , or too complicated t...	In scientific and medical studies , great care must be taken when collecting data to understand the relationship between two variables , such as a drug and its effect on a disease . In any given study there will be many other variables at play , such as the effects of age and sex on the disease . We show that in studie...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "saccharomyces", "homo", "(human)", "computational", "biology" ]	2007	Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis
As targets of adaptive immunity , influenza viruses are characterized by the fluidity with which they respond to the selective pressure applied by neutralizing antibodies . This mutability of structural determinants of protective immunity is the obstacle in developing universal influenza vaccines . Towards the developm...	Influenza viruses remain a formidable public health threat . Because of a dramatic increase in drug resistant strains of influenza viruses and due to the semi-regular emergence of pandemic virus strains , the development of novel antibody-based therapies and influenza vaccine constructs is of great interest . Recently ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "microbiology/immunity", "to", "infections", "virology/vaccines" ]	2010	Broadly Protective Monoclonal Antibodies against H3 Influenza Viruses following Sequential Immunization with Different Hemagglutinins
Chikungunya virus ( CHIKV ) is a mosquito-transmitted alphavirus that can cause fever and chronic arthritis in humans . CHIKV that is generated in mosquito or mammalian cells differs in glycosylation patterns of viral proteins , which may affect its replication and virulence . Herein , we compare replication , pathogen...	Chikungunya virus ( CHIKV ) is a chronic arthritis-causing pathogen in humans , for which no licensed vaccine or specific antiviral drug is currently available . Due to the global spread of its mosquito vectors , CHIKV is now becoming a public health threat worldwide . CHIKV can replicate in both mammalian and mosquito...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Loss of Glycosaminoglycan Receptor Binding after Mosquito Cell Passage Reduces Chikungunya Virus Infectivity
In response to impending anoxic conditions , denitrifying bacteria sustain respiratory metabolism by producing enzymes for reducing nitrogen oxyanions/-oxides ( NOx ) to N2 ( denitrification ) . Since denitrifying bacteria are non-fermentative , the initial production of denitrification proteome depends on energy from ...	In response to oxygen-limiting conditions , denitrifying bacteria produce a set of enzymes to convert / to N2 via NO and N2O . The process ( denitrification ) helps generate energy for survival and growth during anoxia . Denitrification is imperative for the nitrogen cycle and has far-reaching consequences including co...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "bacteriology", "microbial", "metabolism", "ecology", "and", "environmental", "sciences", "environmental", "impacts", "population", "dynamics", "microbiology", "computerized", "simulations", "developmental", "biology", "population", "modeling", "population", "biology", "micro...	2014	Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification
Invasive aspergillosis ( IA ) is a common and life-threatening infection in immunocompromised individuals . A number of environmental and epidemiologic risk factors for developing IA have been identified . However , genetic factors that affect risk for developing IA have not been clearly identified . We report that hos...	Invasive aspergillosis ( IA ) is the most common invasive mould infection among highly immune compromised hosts . While exogenous immune suppression is the greatest risk factor for infection acquisition , polymorphic variation in key immune effector genes likely contributes to disease susceptibility as well . We hypoth...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/fungal", "infections", "genetics", "and", "genomics/complex", "traits", "oncology/hematological", "malignancies" ]	2008	Plasminogen Alleles Influence Susceptibility to Invasive Aspergillosis
Concerns over the possibility of resistance developing to praziquantel ( PZQ ) , has stimulated efforts to develop new drugs for schistosomiasis . In addition to the development of improved whole organism screens , the success of RNA interference ( RNAi ) in schistosomes offers great promise for the identification of p...	Schistosomiasis is a neglected tropical disease affecting 200 million people in the poorest areas of the world . To date no vaccine exists against this parasitosis , and the only possible cure relies on the use of the one available drug , praziquantel . Praziquantel is a safe and effective drug active against adult wor...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Application of RNAi to Genomic Drug Target Validation in Schistosomes
Disruption of protein homeostasis in chloroplasts impairs the correct functioning of essential metabolic pathways , including the methylerythritol 4-phosphate ( MEP ) pathway for the production of plastidial isoprenoids involved in photosynthesis and growth . We previously found that misfolded and aggregated forms of t...	Chloroplasts are central metabolic factories for plant cells . Yet , they are constantly challenged by stress episodes that alter protein homeostasis and disrupt normal chloroplast functions . To deal with this problem , protein quality control pathways involving particular chaperones and proteases promote correct prot...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cellular", "stress", "responses", "enzymes", "plant", "cell", "biology", "gene", "regulation", "regulatory", "proteins", "brassica", "enzymology", "dna-binding", "proteins", "chloroplasts", "cell", "processes", "pigments", "plant", "science", "model", "organisms", "mat...	2017	Interference with plastome gene expression and Clp protease activity in Arabidopsis triggers a chloroplast unfolded protein response to restore protein homeostasis
Metabolic homeostasis and circadian rhythms are closely intertwined biological processes . Nuclear receptors , as sensors of hormonal and nutrient status , are actively implicated in maintaining this physiological relationship . Although the orphan nuclear receptor estrogen-related receptor α ( ERRα , NR3B1 ) plays a c...	The molecular basis for coordinated control of circadian rhythms and metabolism is not well understood . Although integral components of the molecular clock such as the transcription factor BMAL1 can directly regulate some metabolic genes , the output from the circadian oscillator is believed to be in large part mediat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genetics", "and", "genomics", "biology", "genomics", "metabolic", "disorders" ]	2011	Genomic Convergence among ERRα, PROX1, and BMAL1 in the Control of Metabolic Clock Outputs
Bacterial contact-dependent growth inhibition ( CDI ) is mediated by the CdiA/CdiB family of two-partner secretion proteins . Each CdiA protein exhibits a distinct growth inhibition activity , which resides in the polymorphic C-terminal region ( CdiA-CT ) . CDI+ cells also express unique CdiI immunity proteins that spe...	Recent work from our laboratories has shown that many bacteria express contact-dependent growth inhibition ( CDI ) systems in which stick-like proteins on the cell surface deliver toxic tips into target cells . Over 60 distinct toxic tips have been identified in bacteria , and our data indicate that each CDI+ cell expr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "gene", "identification", "and", "analysis", "genetics", "molecular", "genetics", "biology", "genomics", "comparative", "genomics", "microbiology", "bacterial", "biochemistry", "microbial", "growth", "and", "development", "genetics", "and", "genomics", "ge...	2011	Identification of Functional Toxin/Immunity Genes Linked to Contact-Dependent Growth Inhibition (CDI) and Rearrangement Hotspot (Rhs) Systems
Mutations in the human MECP2 gene cause Rett syndrome ( RTT ) , a severe neurodevelopmental disorder that predominantly affects girls . Despite decades of work , the molecular function of MeCP2 is not fully understood . Here we report a systematic identification of MeCP2-interacting proteins in the mouse brain . In add...	Rett syndrome ( RTT ) is a debilitating neurodevelopmental disorder with no cure or effective treatment . To fully understand the disease mechanism and develop therapies , it is necessary to study all aspects of the molecular function of methyl-CpG binding protein 2 ( MeCP2 ) , mutations in which have been identified a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "regulation", "neuroscience", "alternative", "splicing", "animal", "models", "model", "organisms", "mammalian", "genomics", "epigenetics", "dna", "chromatin", "dna", "methylation", "research", "and", "analysis", "methods", "genomic", "signal", "processing", "ani...	2016	Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome
The INhibitor of Growth ( ING ) proteins act as type II tumor suppressors and epigenetic regulators , being stoichiometric members of histone acetyltransferase and histone deacetylase complexes . Expression of the alternatively spliced ING1a tumor suppressor increases >10-fold during replicative senescence . ING1a over...	Alternative splicing of several genes including the p16 and p53 tumor suppressors has been reported to increase during replicative senescence of normal diploid cells , but the biological functions of most alternative transcripts are unknown . We have found that a splicing product of the ING1 epigenetic regulator , ING1...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mitogenic", "signaling", "protein", "interactions", "regulatory", "proteins", "dna", "transcription", "histone", "modification", "membrane", "receptor", "signaling", "cell", "growth", "chromatin", "signaling", "in", "cellular", "processes", "proteins", "gene", "expressio...	2013	The ING1a Tumor Suppressor Regulates Endocytosis to Induce Cellular Senescence Via the Rb-E2F Pathway
Major depressive disorder ( MDD ) associated with chronic neglected tropical diseases ( NTDs ) has been identified as a significant and overlooked contributor to overall disease burden . Cutaneous leishmaniasis ( CL ) is one of the most prevalent and stigmatising NTDs , with an incidence of around 1 million new cases o...	Cutaneous leishmaniasis is a highly prevalent vector-borne disease affecting large parts of Latin America and the Middle East , as well as parts of Northern Africa . There are several types of Cutaneous leishmaniasis , almost all of which have an active phase characterized by a disfiguring lesion ( typically on exposed...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "face", "tropical", "diseases", "parasitic", "diseases", "health", "care", "global", "health", "neglected", "tropical", "diseases", "mood", "disorders", "public", "and", "occupational", "health", "infectious", "diseases", "zoon...	2019	Cutaneous leishmaniasis and co-morbid major depressive disorder: A systematic review with burden estimates
Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases . Here , we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences . The constructed similarity matrix of 62 proteases can be used to intuitiv...	We present a novel approach to intuitively map the degradome , the set of proteolytic enzymes , based on their substrates rather than on the protease sequences . Information stored in cleavage site sequence logos is extracted and transferred into a metric for similarity in protease substrate recognition . By capturing ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos
Plant development is remarkably plastic but how precisely can the plant customize its form to specific environments ? When the plant adjusts its development to different environments , related traits can change in a coordinated fashion , such that two traits co-vary across many genotypes . Alternatively , traits can va...	Plants can dramatically alter their development in order to cope with new environmental conditions . Such plasticity is especially evident in the root system since it adopts a particular architecture under one condition , but can change architecture by altering the extent of lateral root branching in a different condit...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Plasticity Regulators Modulate Specific Root Traits in Discrete Nitrogen Environments
We characterise the evolutionary dynamics of influenza infection described by viral sequence data collected from two challenge studies conducted in human hosts . Viral sequence data were collected at regular intervals from infected hosts . Changes in the sequence data observed across time show that the within-host evol...	The influenza virus is an important cause of disease in the human population . During the course of an infection the virus can evolve rapidly . An important mechanism of viral evolution is reassortment , whereby different segments of the influenza genome are shuffled with other segments , producing new viral combinatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "influenza", "pathogens", "microbiology", "orthomyxoviruses", "alleles", "genetic", "mapping", "viruses", "linkage", "disequilibrium", "rna", "viruses", "micr...	2017	The effective rate of influenza reassortment is limited during human infection
Rapidly increasing temperatures in the mountain region of Nepal and recent reports of dengue fever and lymphatic filariasis cases from mountainous areas of central Nepal prompted us to study the spatio-temporal distribution of the vectors of these two diseases along an altitudinal transect in central Nepal . We conduct...	Dengue fever , a viral disease transmitted by the bites of infected Aedes aegypti and Aedes albopictus mosquitoes , has been rapidly spreading in Nepal since it was first reported in this country in 2004 . Similarly , lymphatic filariasis , a parasitic disease transmitted by Culex quinquefasciatus mosquitoes in Nepal ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "hydrology", "people", "and", "places", "public", "and", "occupational", "health", "geography", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "social", "sciences", "ecology", "science", "policy", "epidemiology", "earth", "scie...	2014	Spatio-Temporal Distribution of Dengue and Lymphatic Filariasis Vectors along an Altitudinal Transect in Central Nepal
The genome-sequencing gold rush has facilitated the use of comparative genomics to uncover patterns of genome evolution , although their causal mechanisms remain elusive . One such trend , ubiquitous to prokarya and eukarya , is the association of insertion/deletion mutations ( indels ) with increases in the nucleotide...	An intriguing observation made during the comparison of genomes is that insertion and deletion mutations ( indels ) cluster together with nucleotide substitutions . Two ( not mutually exclusive ) hypotheses have been proposed to explain this phenomenon . The first postulates that an indel mutation causes an increase in...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", ...	2011	Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences
HIV and SIV infection dynamics are commonly investigated by measuring plasma viral loads . However , this total viral load value represents the sum of many individual infection events , which are difficult to independently track using conventional sequencing approaches . To overcome this challenge , we generated a gene...	Elucidation of HIV dynamics is essential for a thorough understanding of viral transmission , therapeutic interventions , pathogenesis , and immune evasion . The complex dynamics of reservoir establishment and viral recrudescence upon therapy removal present the primary obstacles to developing a functional cure . We so...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "viral", "transmission", "and", "infection", "microbiology", "vertebrates", "animals", "mammals", "primates", "animal", "models", "experimental", "organism", "systems", "microbial", "genetics", "viral", "load", ...	2017	Genetically-barcoded SIV facilitates enumeration of rebound variants and estimation of reactivation rates in nonhuman primates following interruption of suppressive antiretroviral therapy
Pathogen clearance and host resilience/tolerance to infection are both important factors in surviving an infection . Cells of the myeloid lineage play important roles in both of these processes . Neutrophils , monocytes , macrophages , and dendritic cells all have important roles in initiation of the immune response an...	Multicellular organisms are constantly interacting with microbes . Pathogens are microbes that can cause harm to the host if not properly controlled , therefore pathogen clearance is an essential part of survival of all multi-cellular organisms . Equally important factors in survival are host resilience mechanisms , or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "immunology", "microbiology", "bone", "marrow", "cells", "animal", "models", "streptococcus",...	2016	The Influence of Programmed Cell Death in Myeloid Cells on Host Resilience to Infection with Legionella pneumophila or Streptococcus pyogenes
RNA viruses are the only known RNA-protein ( RNP ) entities capable of autonomous replication ( albeit within a permissive host environment ) . A 33 . 5 kilobase ( kb ) nidovirus has been considered close to the upper size limit for such entities; conversely , the minimal cellular DNA genome is in the 100–300 kb range ...	RNA viruses are the only known RNA-protein ( RNP ) entities capable of autonomous replication . The upper genome size for such entities was assumed to be <35 kb; conversely , the minimal cellular DNA genome is in the 100–300 kilobase ( kb ) range . This large difference presents a daunting gap for the proposed evolutio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "invertebrates", "microbiology", "animals", "invertebrate", "genomics", "viruses", "phylogenetics", "data", "management", "rna", "viruses", "phylogenetic", "analysis", "genome", "analysis", "planarians", "microbial", "genomics", "viral", "genomics", "computer", ...	2018	A planarian nidovirus expands the limits of RNA genome size
Phytopathogenic ascomycete fungi possess huge effector repertoires that are dominated by hundreds of sequence-unrelated small secreted proteins . The molecular function of these effectors and the evolutionary mechanisms that generate this tremendous number of singleton genes are largely unknown . To get a deeper unders...	Fungal plant pathogens are of outstanding economic and ecological importance and cause destructive diseases on many cultivated and wild plants . Effector proteins that are secreted during infection to manipulate the host and to promote disease are a key element in fungal virulence . Phytopathogenic fungi possess huge e...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi
Trachoma is the leading infectious cause of blindness in the world and is associated with precarious living conditions in developing countries . The aim of the present study was to evaluate the prevalence of trachoma in three municipalities of the Marajó Archipelago , located in the state of Pará , Brazil . In 2008 , 2...	Trachoma is one of the main neglected infectious diseases and carry a considerable burden to human health as a consequence of the clinical severity of the disease which may evolve to blindness . The lack of hygiene , education and other indicators of low social and economic markers occurring in developing and underdeve...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schoolchildren", "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "education", "chlamydia", "trachomatis", "pathogens", "sociology", "tropical", "diseases", "microbiology", "geographical", "locations", "social", "sciences",...	2018	Prevalence of trachoma in school children in the Marajó Archipelago, Brazilian Amazon, and the impact of the introduction of educational and preventive measures on the disease over eight years
The nematode intestine is a tissue of interest for developing new methods of therapy and control of parasitic nematodes . However , biological details of intestinal cell functions remain obscure , as do the proteins and molecular functions located on the apical intestinal membrane ( AIM ) , and within the intestinal lu...	Past research has demonstrated that the nematode intestine has value for developing new methods of therapy and control of parasitic nematodes , as related to both vaccines and other anthelmintics . Yet , information related to basic intestinal cell biology is very limited . Research progress reported here moves towards...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "enzymes", "tropical", "diseases", "enzymology", "parasitic", "diseases", "animals", "parasitology", "parasite", "physiology", "neglected", "tropical", "diseases", "digestive", "enzymes", "soil-transmitt...	2015	Peptidases Compartmentalized to the Ascaris suum Intestinal Lumen and Apical Intestinal Membrane
Genes required for infection of mice by Salmonella Typhimurium can be identified by the interrogation of random transposon mutant libraries for mutants that cannot survive in vivo . Inactivation of such genes produces attenuated S . Typhimurium strains that have potential for use as live attenuated vaccines . A quantit...	Salmonella Typhimurium infection of mice is an established model of systemic typhoid fever in humans . Mutations that inactivate genes that are important for virulence produce attenuated S . Typhimurium bacteria that have potential for use as live vaccines . To investigate the infection process we have produced a large...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genomics", "microbiology/immunity", "to", "infections", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/gene", "function", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/bact...	2009	Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Staphylococcus aureus is a prominent bacterial pathogen that is known to agglutinate in the presence of human plasma to form stable clumps . There is increasing evidence that agglutination aids S . aureus pathogenesis , but the mechanisms of this process remain to be fully elucidated . To better define this process , w...	Staphylococcus aureus is a bacterial pathogen that is responsible for causing significant disease in humans . The development of antibiotic resistant strains has made these infections more difficult to treat , and an improved understanding of how this pathogen causes infections will facilitate the development of new to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Staphylococcus aureus ArlRS Two-Component System Is a Novel Regulator of Agglutination and Pathogenesis
Kaposi’s Sarcoma associated Herpesvirus ( KSHV ) , an oncogenic , human gamma-herpesvirus , is the etiological agent of Kaposi’s Sarcoma the most common tumor of AIDS patients world-wide . KSHV is predominantly latent in the main KS tumor cell , the spindle cell , a cell of endothelial origin . KSHV modulates numerous ...	Kaposi’s Sarcoma herpesvirus ( KSHV ) is the etiologic agent of Kaposi’s Sarcoma , the most common tumor of AIDS patients . KSHV modulates host cell signaling and metabolism to maintain a life-long latent infection . To unravel the underlying cellular mechanisms modulated by KSHV , we used multiple global systems biolo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "endothelial", "cells", "protein", "interaction", "networks", "pathogens", "microbiology", "epithelial", "cells", "viruses", "dna", "viruses", "network", "analysi...	2017	Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism
To work towards reaching the WHO goal of eliminating soil-transmitted helminth ( STH ) infections as a public health problem , the total number of children receiving anthelmintic drugs has strongly increased over the past few years . However , as drug pressure levels rise , the development of anthelmintic drug resistan...	Soil-transmitted helminths ( STHs ) affect 1 . 4 billion people worldwide and cause significant morbidity when the intensity of infection is high . Currently , these infections are controlled in school-aged children by preventive chemotherapy with the benzimidazole drugs albendazole ( ALB ) or mebendazole ( MEB ) . How...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "hookworms", "parasitic", "diseases", "animals", "mathematics", "pharmaceutics", "drug", "administration", "neglected", "tropical", "diseases", "pharmacology", "extraction", "tech...	2018	Comprehensive evaluation of stool-based diagnostic methods and benzimidazole resistance markers to assess drug efficacy and detect the emergence of anthelmintic resistance: A Starworms study protocol
Multiple genome-wide association studies ( GWAS ) have been performed in HIV-1 infected individuals , identifying common genetic influences on viral control and disease course . Similarly , common genetic correlates of acquisition of HIV-1 after exposure have been interrogated using GWAS , although in generally small s...	Comparing the frequency differences between common DNA variants in disease-affected cases and in unaffected controls has been successful in uncovering the genetic component of multiple diseases . This approach is most effective when large samples of cases and controls are available . Here we combine information from mu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "hiv", "genetics", "biology", "genomics", "viral", "diseases" ]	2013	Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls
When organisms need to perform multiple tasks they face a fundamental tradeoff: no phenotype can be optimal at all tasks . This situation was recently analyzed using Pareto optimality , showing that tradeoffs between tasks lead to phenotypes distributed on low dimensional polygons in trait space . The vertices of these...	Understanding why some mammals live longer than others is of crucial interest . Here we study how longevity relates to other life-history traits , using data on about 2000 species of mammals and birds . In contrast to the tradition in which traits fall on a line in logarithmic coordinates , called allometric lines . We...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space
Dynamic exchange of a subset of nucleosomes in vivo plays important roles in epigenetic inheritance of chromatin states , chromatin insulator function , chromosome folding , and the maintenance of the pluripotent state of embryonic stem cells . Here , we extend a pulse-chase strategy for carrying out genome-wide measur...	The ability of cells to remember the correct cell fate is at least partly dependent on how the genome is packaged . Embryonic stem ( ES ) cells , which have the ability to become any cell type in the body , are a particularly well-studied system for understanding how the packaging of the genome – chromatin – controls c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "expression", "genetics", "epigenetics", "biology", "and", "life", "sciences", "molecular", "genetics" ]	2014	A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters
The cyclin-dependent kinase inhibitor p27KIP1 is a tumor suppressor gene in mice , and loss of p27 protein is a negative prognostic indicator in human cancers . Unlike other tumor suppressors , the p27 gene is rarely mutated in tumors . Therefore misregulation of p27 , rather than loss of the gene , is responsible for ...	Many human cancers express abnormally low amounts of the p27 protein , and this is associated with aggressive tumor behavior and a poor clinical outcome . Surprisingly , the p27 gene is rarely mutated in these tumors and retains the potential to produce normal amounts of p27 protein . Therefore , understanding the path...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "mus", "(mouse)", "oncology", "genetics", "and", "genomics", "immunology" ]	2007	A Mechanism Misregulating p27 in Tumors Discovered in a Functional Genomic Screen
Loiasis , a filarial infection caused by Loa loa usually thought to cause relatively minor morbidity , can cause serious and often fatal reactions in patients carrying very high levels of circulating Loa loa microfilariae ( mf ) following administration of microfilaricidal drugs . An experimental model of this conditio...	Loiasis is a filarial infection of humans that , in addition to causing severe direct clinical effects , is of concern to the global community’s efforts to eliminate the important filarial diseases , onchocerciasis and lymphatic filariasis , through causing interruption to mass drug distribution activities . Hyper-micr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Parasitological, Hematological and Biochemical Characteristics of a Model of Hyper-microfilariaemic Loiasis (Loa loa) in the Baboon (Papio anubis)
Snakebite envenoming ( SBE ) is a major problem in rural areas of West Africa ( WA ) . Compared to other Neglected Tropical Diseases ( NTD ) , the public health burden of SBE has not been well characterized . We estimated the impact of snakebite mortality and morbidity using the Disability Adjusted Life Years ( DALYs )...	Snakebite envenoming ( SBE ) is a major problem in rural West Africa ( WA ) . However , despite the high incidence of SBE in this region , government funding for the prevention or treatment of SBE is generally limited . In this analysis , we attempted to estimate how the public health burden of SBE compares to other mo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Snakebite is Under Appreciated: Appraisal of Burden from West Africa
Identification of cellular receptors and characterization of viral tropism in animal models have vastly improved our understanding of morbillivirus pathogenesis . However , specific aspects of viral entry , dissemination and transmission remain difficult to recapitulate in animal models . Here , we used three virologic...	Canine distemper virus ( CDV ) infection of ferrets is a tractable animal model for measles . Ferrets are highly susceptible to CDV , and inoculation with a low dose leads to lethal disease . We performed in vivo competition experiments to study virus entry , dissemination and transmission . Ferrets were simultaneously...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "methods" ]	[ "flow", "cytometry", "medicine", "and", "health", "sciences", "nose", "face", "pathology", "and", "laboratory", "medicine", "pathogens", "canine", "distemper", "virus", "microbiology", "vertebrates", "light", "microscopy", "orthomyxoviruses", "animals", "mammals", "viru...	2017	Delineating morbillivirus entry, dissemination and airborne transmission by studying in vivo competition of multicolor canine distemper viruses in ferrets
The rarity of beneficial mutations has frustrated efforts to develop a quantitative theory of adaptation . Recent models of adaptive walks , the sequential substitution of beneficial mutations by selection , make two compelling predictions: adaptive walks should be short , and fitness increases should become exponentia...	Adaptation is one of the least understood processes in biology because it relies on beneficial mutations , which are often too rare to study . We developed a method to infer the number and size of beneficial mutations substituted during adaptation , a process called an adaptive walk , and used this to test predictions ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "and", "genomics", "microbiology" ]	2009	The Properties of Adaptive Walks in Evolving Populations of Fungus
Human antibody 10E8 targets the conserved membrane proximal external region ( MPER ) of envelope glycoprotein ( Env ) subunit gp41 and neutralizes HIV-1 with exceptional potency . Remarkably , HIV-1 containing mutations that reportedly knockout 10E8 binding to linear MPER peptides are partially neutralized by 10E8 , pr...	As vaccination , immunoprophylaxis and immunotherapies are becoming increasingly feasible approaches to combat HIV/AIDS , understanding the activity of relevant anti-HIV antibodies is crucial . Antibody 10E8 defines a key vulnerability on the envelope spikes of a vast majority of HIV isolates but mechanisms of resistan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunodeficiency", "viruses", "infectious", "diseases", "medicine", "and", "health", "sciences", "medical", "microbiology", "hiv", "viral", "pathogens", "microbial", "pathogens", "biology", "and", "life", "sciences", "immunology", "microbiology", "viral", "diseases" ]	2014	Antibody to gp41 MPER Alters Functional Properties of HIV-1 Env without Complete Neutralization
Fes1 is a conserved armadillo repeat-containing Hsp70 nucleotide exchange factor important for growth at high temperature , proteasomal protein degradation and prion propagation . Depleting or mutating Fes1 induces a stress response and causes defects in these processes that are ascribed solely to disruption of Fes1 re...	Fes1 , a yeast homolog of human nucleotide exchange factor HspBP1 , binds and regulates Hsp70 , a universally conserved protein that helps maintain health of proteins in cells . Fes1 is believed to function only by helping Hsp70 release ADP and substrates and cells lacking Fes1 are sick . We find Fes1 is essential for ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "walls", "protein", "interactions", "chemical", "compounds", "membrane", "staining", "vertebrates", "carbohydrates", "organic", "compounds", "glucose", "animals", "mammals", "xenarthra", "cell", "signaling", "fungi", "cellular", "structures", "and", "organelles", ...	2019	Hsp70-nucleotide exchange factor (NEF) Fes1 has non-NEF roles in degradation of gluconeogenic enzymes and cell wall integrity
The entropy metric derived from information theory provides a means to quantify the amount of information transmitted in acoustic streams like speech or music . By systematically varying the entropy of pitch sequences , we sought brain areas where neural activity and energetic demands increase as a function of entropy ...	Understanding how the brain makes sense of our acoustic environment remains a major challenge . One way to describe the complexity of our acoustic environment is in terms of information entropy: acoustic signals with high entropy convey large amounts of information , whereas low entropy signifies redundancy . To invest...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "computational", "biology" ]	2007	An Information Theoretic Characterisation of Auditory Encoding
The hemolytic uremic syndrome ( HUS ) is characterized by hemolytic anemia , thrombocytopenia and renal dysfunction . The typical form of HUS is generally associated with infections by Gram-negative Shiga toxin ( Stx ) -producing Escherichia coli ( STEC ) . Endothelial dysfunction induced by Stx is central , but bacter...	Hemolytic-uremic syndrome ( HUS ) is generally caused by Shiga toxin ( Stx ) -producing Escherichia coli but bacterial lipopolysaccharide ( LPS ) and neutrophils ( PMN ) contribute to the pathophysiology . Acute renal failure is the main feature of HUS , but in severe cases , patients develop neurological complications...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases" ]	2012	Shiga Toxin 1 Induces on Lipopolysaccharide-Treated Astrocytes the Release of Tumor Necrosis Factor-alpha that Alter Brain-Like Endothelium Integrity
BRIT1 protein ( also known as MCPH1 ) contains 3 BRCT domains which are conserved in BRCA1 , BRCA2 , and other important molecules involved in DNA damage signaling , DNA repair , and tumor suppression . BRIT1 mutations or aberrant expression are found in primary microcephaly patients as well as in cancer patients . Rec...	The repair of DNA breaks in cells is critical for maintaining genomic integrity and suppressing tumor development . DNA breaks can arise from exogenous agents such as ionizing radiation ( IR ) or can form during the process of germ cell ( sperm and egg ) generation . BRIT1 protein ( also known as MCPH1 ) is a recently ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics/cancer", "genetics" ]	2010	BRIT1/MCPH1 Is Essential for Mitotic and Meiotic Recombination DNA Repair and Maintaining Genomic Stability in Mice
Epigenetic gene silencing plays a critical role in regulating gene expression and contributes to organismal development and cell fate acquisition in eukaryotes . In fission yeast , Schizosaccharomyces pombe , heterochromatin-associated gene silencing is known to be mediated by RNA processing pathways including RNA inte...	Epigenetic mechanisms regulate when , where , and how an organism uses the genetic information stored in its genome . They are essential to many cellular processes , such as the regulation of gene expression , genome organization , and cell-fate determination . They also govern growth , development , and ultimately hum...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "interference", "gene", "regulation", "reporter", "genes", "fungi", "model", "organisms", "gene", "types", "epigenetics", "chromatin", "schizosaccharomyces", "heterochromatin", "research", "and", "analysis", "methods", "small", "interfering", "rnas", "chromosome", ...	2016	A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5’-3’ Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe
In a murine model of repeated exposure of the skin to infective Schistosoma mansoni cercariae , events leading to the priming of CD4 cells in the skin draining lymph nodes were examined . The dermal exudate cell ( DEC ) population recovered from repeatedly ( 4x ) exposed skin contained an influx of mononuclear phagocyt...	In areas endemic for schistosomiasis , repeated exposure to infective cercariae is a frequent occurrence , and repeated exposure of murine skin to Schistosoma mansoni resulted in CD4+ T cells becoming hypo-responsive . Here potential contributory mechanisms were investigated . In the skin infection site , three mononuc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "dermatology", "invertebrates", "schistosoma", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "cell", "death", "immune", "cells", "helminths", "immunology", "cell", "processes", "animals", "skin", "infections", "phagocytes", "infect...	2016	Alternatively Activated Mononuclear Phagocytes from the Skin Site of Infection and the Impact of IL-4Rα Signalling on CD4+T Cell Survival in Draining Lymph Nodes after Repeated Exposure to Schistosoma mansoni Cercariae
Parasitic protozoa , such as Leishmania species , are thought to express a number of surface and secreted nucleoside triphosphate diphosphohydrolases ( NTPDases ) which hydrolyze a broad range of nucleoside tri- and diphosphates . However , the functional significance of NTPDases in parasite virulence is poorly defined...	Nucleoside triphosphate diphosphohydrolases ( NTPDases ) are a family of enzymes expressed in many eukaryotes , ranging from single-celled parasites to mammals . In mammals , NTPDases can have an immunomodulatory role , while in pathogenic protists cell-surface and secreted NTPDases are thought to be important virulenc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "parasitic", "diseases", "molecular", "biology", "parasitology" ]	2014	Golgi-Located NTPDase1 of Leishmania major Is Required for Lipophosphoglycan Elongation and Normal Lesion Development whereas Secreted NTPDase2 Is Dispensable for Virulence
Dosage compensation ensures similar levels of X-linked gene products in males ( XY or XO ) and females ( XX ) , despite their different numbers of X chromosomes . In mammals , flies , and worms , dosage compensation is mediated by a specialized machinery that localizes to one or both of the X chromosomes in one sex res...	In organisms where females have two X chromosomes and males only have one , a mechanism called dosage compensation ensures that both sexes receive the same amount of information from their X chromosomes . Disruption of dosage compensation leads to lethality in the affected sex . While the precise mechanisms of dosage c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "cell", "biology/gene", "expression", "cell", "biology/nuclear", "structure", "and", "function" ]	2009	Restricting Dosage Compensation Complex Binding to the X Chromosomes by H2A.Z/HTZ-1
Over 200 cryptosporidiosis outbreaks have been reported , but little is known if other enteric pathogens were also involved in some of these outbreaks . Recently , an outbreak of cryptosporidiosis linked to poor hygiene by two Cryptosporidium hominis subtypes occurred in a pediatric hospital ward ( Ward A ) in China , ...	The transmission of Giardia duodenalis , Enterocytozoon bieneusi , and Clostridium difficile is poorly understood in developing countries despite their wide occurrence . Because they are transmitted by the same fecal-oral route as Cryptosporidium , in this study , we have examined the occurrence of these enteric pathog...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Concurrent Infections of Giardia duodenalis, Enterocytozoon bieneusi, and Clostridium difficile in Children during a Cryptosporidiosis Outbreak in a Pediatric Hospital in China
Mycobacterium species are grown using specific media that increase laboratory cost , thus hampering their diffusion in resource-limited countries . Preliminary data suggested that versatile blood agar may be also used for mycobacterial culture . We examined the growth of 41 different Mycobacterium species on 5% blood a...	Mycobacteria are organisms responsible for animal and human infections comprising tuberculosis due to Mycobacterium tuberculosis and other opportunistic infections . Such infections require specific antibiotic treatment and prevention of secondary cases in the occurrence of pulmonary tuberculosis . The accurate diagnos...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections" ]	2007	Cost-Effectiveness of Blood Agar for Isolation of Mycobacteria
Many important protein–protein interactions are mediated by the binding of a short peptide stretch in one protein to a large globular segment in another . Recent efforts have provided hundreds of examples of new peptides binding to proteins for which a three-dimensional structure is available ( either known experimenta...	An important class of protein interactions in critical cellular processes , such as signaling pathways , involves a domain from one protein binding to a linear peptide stretch of another . Many methods identify peptides mediating such interactions but without details of how the interactions occur , even when excellent ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "molecular", "biology/bioinformatics", "biophysics/biomacromolecule-ligand", "interactions", "biochemistry/bioinformatics", "biochemistry/drug", "discovery" ]	2009	Accurate Prediction of Peptide Binding Sites on Protein Surfaces
Buruli ulcer , the third mycobacterial disease after tuberculosis and leprosy , is caused by the environmental mycobacterium M . ulcerans . There is at present no clear understanding of the exact mode ( s ) of transmission of M . ulcerans . Populations affected by Buruli ulcer are those living close to humid and swampy...	Buruli ulcer is a neglected tropical disease due to M . ulcerans , an environmental mycobacteria . Modes of transmission to human remain unclear and water bugs and mosquitoes had been incriminated with more or less experimental laboratory evidences and filed studies . In this context , we have investigated the presence...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	A Field Study in Benin to Investigate the Role of Mosquitoes and Other Flying Insects in the Ecology of Mycobacterium ulcerans
Regulatory and developmental systems produce phenotypes that are robust to environmental and genetic variation . A gene product that normally contributes to this robustness is termed a phenotypic capacitor . When a phenotypic capacitor fails , for example when challenged by a harsh environment or mutation , the system ...	Most species maintain abundant genetic variation and experience a wide range of environmental conditions , yet phenotypic differences between individuals are usually small . This phenomenon , known as phenotypic robustness , presents an apparent contradiction: if biological systems are so resistant to variation , how d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "computational", "biology", "evolutionary", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2008	Network Hubs Buffer Environmental Variation in Saccharomyces cerevisiae
Discriminating the causative disease variant ( s ) for individuals with inherited or de novo mutations presents one of the main challenges faced by the clinical genetics community today . Computational approaches for variant prioritization include machine learning methods utilizing a large number of features , includin...	We address the problem of how to distinguish which of the many thousands of DNA sequence variants carried by an individual with a rare disease is responsible for the disease phenotypes . This can help clinicians arrive at a diagnosis , but also can be instrumental in improving our understanding of the pathobiology of t...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "alleles", "animal", "models", "genomic", "databases", "model", "organisms", "drug", "design", "experimental", "organism", "systems", "genome", "analysis", "pharmacology", "computer-a...	2017	Semantic prioritization of novel causative genomic variants
The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments . The Drosophila chromatin remodeling ATPase ISWI plays evolutionarily conserved roles in chromatin organization . Interestingly , ISWI genetically interacts with the hsrω gene ,...	Chromatin structure and function are regulated by the concerted activity of covalent modifiers of chromatin , nucleosome remodeling factors , and several emerging classes of non-coding RNAs . ISWI is an evolutionarily conserved ATP-dependent chromatin remodeler playing essential roles in chromosome condensation , gene ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "expression", "genetics", "epigenetics", "biology", "molecular", "genetics", "genetics", "and", "genomics" ]	2011	The ISWI Chromatin Remodeler Organizes the hsrω ncRNA–Containing Omega Speckle Nuclear Compartments
Meeting the increasing food and energy demands of a growing population will require the development of ground-breaking strategies that promote sustainable plant production . Host-induced gene silencing has shown great potential for controlling pest and diseases in crop plants . However , while delivery of inhibitory no...	RNA interference has emerged as a powerful genetic tool for scientific research . The demonstration that agricultural pests , such as insects and nematodes , are killed by exogenously supplied RNA targeting their essential genes has raised the possibility that plant predation can be controlled by lethal RNA signals . W...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "medicine", "and", "health", "sciences", "fusarium", "barley", "pathology", "and", "laboratory", "medicine", "fungal", "genetics", "gene", "regulation", "pathogens", "microbiology", "fusarium", "graminearum", "cereal", "crops", "fungi", "plant", "s...	2016	An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery
Metastasis is a complex process utilizing both tumor-cell-autonomous properties and host-derived factors , including cellular immunity . We have previously shown that germline polymorphisms can modify tumor cell metastatic capabilities through cell-autonomous mechanisms . However , how metastasis susceptibility genes i...	Metastasis , the dissemination and growth of tumor cells in organs distinct from which they originated , is the most common cause of cancer-related death . Accumulating evidence indicates that an individual's genetic background , the heritable complement of genetic variations that distinguish individuals , not only con...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "cancer", "genetics", "immune", "cells", "genetic", "screens", "genetics", "t", "cells", "immunology", "biology", "genetics", "and", "genomics" ]	2012	Cadm1 Is a Metastasis Susceptibility Gene That Suppresses Metastasis by Modifying Tumor Interaction with the Cell-Mediated Immunity
Epigenetic changes can be induced by adverse environmental exposures , such as nutritional imbalance , but little is known about the nature or extent of these changes . Here we have explored the epigenomic effects of a sustained nutritional change , excess dietary methyl donors , by assessing genomic CpG methylation pa...	Epigenetic changes to gene expression that do not involve changes to DNA sequence can be influenced by the environment and provide one candidate mechanism by which early nutrition can influence adult disease risk . Here , we examined epigenetic changes across the genome in response to short- and long-term exposure to a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "nutrition" ]	2011	A Sustained Dietary Change Increases Epigenetic Variation in Isogenic Mice
A phylogenetically diverse subset of bacterial species are naturally competent for transformation by DNA . Transformation entails recombination of genes between different lineages , representing a form of bacterial sex that increases standing genetic variation . We first assess whether homologous recombination by trans...	In certain environmental conditions , populations of the bacterium Bacillus subtilis split into two physiologically distinct phenotypes . While some cells continue to grow and divide , a minority become “competent” for transformation by extracellular DNA . This differentiation process is driven not by genetic differenc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/sexual", "behavior", "computational", "biology/evolutionary", "modeling", "genetics", "and", "genomics/population", "genetics" ]	2010	Optimal Strategy for Competence Differentiation in Bacteria
MIcrophthalmia-associated Transcription Factor ( MITF ) regulates melanocyte and melanoma physiology . We show that MITF associates the NURF chromatin-remodelling factor in melanoma cells . ShRNA-mediated silencing of the NURF subunit BPTF revealed its essential role in several melanoma cell lines and in untransformed ...	The melanocytes pigmenting the coat of adult mice derive from the melanocyte stem cell population residing in the permanent bulge area of the hair follicle . At each angen phase , melanocyte stem cells are stimulated to generate proliferative transient amplifying cells that migrate to the bulb of the follicle where the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Chromatin-Remodelling Complex NURF Is Essential for Differentiation of Adult Melanocyte Stem Cells
In mammalian oocytes , three actin binding proteins , Formin 2 ( Fmn2 ) , Spire , and profilin , synergistically organize a dynamic cytoplasmic actin meshwork that mediates translocation of the spindle toward the cortex and is required for successful fertilization . Here we characterize Fmn2 and elucidate the molecular...	Mammalian reproduction requires successful meiosis , which consists of two strongly asymmetric cell divisions . In meiosis I , movement of the spindle ( the subcellular structure that segregates chromosomes during division ) toward the oocyte cortex ( the outer layer of the egg ) is essential for fertility . This proce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "biochemistry", "developmental", "biology", "biology", "molecular", "cell", "biology", "biophysics" ]	2014	Spire and Formin 2 Synergize and Antagonize in Regulating Actin Assembly in Meiosis by a Ping-Pong Mechanism
Bloodstream-form African trypanosomes encode two structurally related glycosylphosphatidylinositol ( GPI ) -anchored proteins that are critical virulence factors , variant surface glycoprotein ( VSG ) for antigenic variation and transferrin receptor ( TfR ) for iron acquisition . Both are transcribed from the active te...	African trypanosomes , protozoan parasites that cause African Sleeping Sickness , have two structurally related secretory proteins that are critical for their success as pathogens: variant surface glycoprotein ( VSG ) , which is responsible for evasion of host immune responses , and transferrin receptor ( TfR ) , which...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "lysosomes", "rna", "interference", "membrane", "proteins", "immunoprecipitation", "epigenetics", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "sequence", "analysis", "specimen", "preparation", "and", "treat...	2017	Controlling transferrin receptor trafficking with GPI-valence in bloodstream stage African trypanosomes
Alternative splicing of messenger RNA can generate a wide variety of mature RNA transcripts , and these transcripts may produce protein isoforms with diverse cellular functions . While there is much supporting evidence for the expression of alternative transcripts , the same is not true for the alternatively spliced pr...	Alternative splicing is thought to be one means for generating the protein diversity necessary for the whole range of cellular functions . While the presence of alternatively spliced transcripts in the cell has been amply demonstrated , the same cannot be said for alternatively spliced proteins . The quest for alternat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level
Chlamydia trachomatis is the etiological agent of trachoma the world's leading cause of infectious blindness . Here , we investigate whether protracted clearance of a primary infection in nonhuman primates is attributable to antigenic variation or related to the maturation of the anti-chlamydial humoral immune response...	Chlamydia trachomatis is the etiological agent of trachoma the world's leading cause of infectious blindness . In this study , we investigated whether delayed clearance of a primary infection in nonhuman primates was attributable to antigenic variation or related to gradual changes in the humoral immune response specif...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "trachoma" ]	2013	Antibody Signature of Spontaneous Clearance of Chlamydia trachomatis Ocular Infection and Partial Resistance against Re-challenge in a Nonhuman Primate Trachoma Model
The emergence of infectious diseases of zoonotic origin highlights the need to understand social practices at the animal-human interface . This study provides a qualitative account of interactions between humans and wild animals in predominantly Mende villages of southern Sierra Leone . We conducted fieldwork over 4 mo...	Studying how and why humans interact with animals is important to understand the transmission of zoonotic diseases ( infectious diseases transmitted from animals to humans ) and how to prevent and control them . We conducted a qualitative study to understand how and why people come into contact with wild animals in the...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "animal", "types", "children", "medicine", "and", "health", "sciences", "zoonotic", "pathogens", "animal", "pathogens", "pathology", "and", "laboratory", "medicine", "pathogens", "diet", "vertebrates", "animals", "mammals", "animal", "products", "age", "groups", "nutr...	2017	Participation of women and children in hunting activities in Sierra Leone and implications for control of zoonotic infections
RNAi screens have , to date , identified many genes required for mitotic divisions of Drosophila tissue culture cells . However , the inventory of such genes remains incomplete . We have combined the powers of bioinformatics and RNAi technology to detect novel mitotic genes . We found that Drosophila genes involved in ...	Mitosis is the evolutionarily conserved process that enables a dividing cell to equally partition its genetic material between the two daughter cells . The fidelity of mitotic division is crucial for normal development of multicellular organisms and to prevent cancer or birth defects . Understanding the molecular mecha...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/functional", "genomics" ]	2008	Identification of Drosophila Mitotic Genes by Combining Co-Expression Analysis and RNA Interference
During meiosis , repair of programmed DNA double-strand breaks ( DSBs ) by recombination promotes pairing of homologous chromosomes and their connection by crossovers . Two DNA strand-exchange proteins , Rad51 and Dmc1 , are required for meiotic recombination in many organisms . Studies in budding yeast imply that Rad5...	Meiosis is the specialized cell division that produces gametes by precisely reducing the chromosome copy number from two to one . Accurate segregation of homologous chromosome pairs requires they be connected by crossing-over , the precise breakage and exchange of chromosome arms that is carried out by a process called...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Meiotic Crossover Control by Concerted Action of Rad51-Dmc1 in Homolog Template Bias and Robust Homeostatic Regulation

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